Simplified DGS procedure for large-scale genome structural study

Yong Chul Jung; Jia Xu; Jun Chen; Yeong C. Kim; David J. Winchester; San Ming Wang

doi:10.2144/000113294

Simplified DGS procedure for large-scale genome structural study

Yong Chul Jung, Jia Xu, Jun Chen, Yeong C. Kim, David J. Winchester, San Ming Wang

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Ditag genome scanning (DGS) uses next-generation DNA sequencing to sequence the ends of ditag fragments produced by restriction enzymes. These sequences are compared to known genome sequences to determine their structure. In order to use DGS for large-scale genome structural studies, we have substantially revised the original protocol by replacing the in vivo genomic DNA cloning with in vitro adaptor ligation, eliminating the ditag concatemerization steps, and replacing the 454 sequencer with Solexa or SOLiD sequencers for ditag sequence collection. This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously.

Original language	English (US)
Pages (from-to)	969-971
Number of pages	3
Journal	BioTechniques
Volume	47
Issue number	5
DOIs	https://doi.org/10.2144/000113294
State	Published - Nov 2009
Externally published	Yes

Keywords

Ditag
Genome structure
Next-generation DNA sequencer
Paired-end
Restriction fragment

ASJC Scopus subject areas

Biotechnology
General Biochemistry, Genetics and Molecular Biology

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10.2144/000113294

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title = "Simplified DGS procedure for large-scale genome structural study",

abstract = "Ditag genome scanning (DGS) uses next-generation DNA sequencing to sequence the ends of ditag fragments produced by restriction enzymes. These sequences are compared to known genome sequences to determine their structure. In order to use DGS for large-scale genome structural studies, we have substantially revised the original protocol by replacing the in vivo genomic DNA cloning with in vitro adaptor ligation, eliminating the ditag concatemerization steps, and replacing the 454 sequencer with Solexa or SOLiD sequencers for ditag sequence collection. This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously.",

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author = "Jung, {Yong Chul} and Jia Xu and Jun Chen and Kim, {Yeong C.} and Winchester, {David J.} and Wang, {San Ming}",

year = "2009",

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doi = "10.2144/000113294",

language = "English (US)",

volume = "47",

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T1 - Simplified DGS procedure for large-scale genome structural study

AU - Jung, Yong Chul

AU - Xu, Jia

AU - Chen, Jun

AU - Kim, Yeong C.

AU - Winchester, David J.

AU - Wang, San Ming

PY - 2009/11

Y1 - 2009/11

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AB - Ditag genome scanning (DGS) uses next-generation DNA sequencing to sequence the ends of ditag fragments produced by restriction enzymes. These sequences are compared to known genome sequences to determine their structure. In order to use DGS for large-scale genome structural studies, we have substantially revised the original protocol by replacing the in vivo genomic DNA cloning with in vitro adaptor ligation, eliminating the ditag concatemerization steps, and replacing the 454 sequencer with Solexa or SOLiD sequencers for ditag sequence collection. This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously.

KW - Ditag

KW - Genome structure

KW - Next-generation DNA sequencer

KW - Paired-end

KW - Restriction fragment

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Simplified DGS procedure for large-scale genome structural study

Abstract

Keywords

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